Introduction

The TIES VM snapshot is a Ubuntu Linux VM that has all the TIES software installed and configured. We preloaded 11,149 TCGA reports yielding an estimated database size of 2 GB. You will be able to add your own documents to TIES and have them processed and searchable through the TIES client installed in the VM.

Requirements

• 20GB Disk Space
• 8GB RAM
• VMware Workstation or Oracle VM VirtualBox

Step 1: Download and install a VM hypervisor

The TIES VM snapshot requires the a VM hypervisor(such as VMware Workstation or Oracle VM VirtualBox) to run. Download and install it before your proceed.

Step 2: Download and unzip the VM

DOWNLOAD HERE

The TIES VM is distributed as a tar file. Download and untar it to a location on your hard disk. The unzipped directory takes 16GB of space.

Step 3: Log into VM

You can run the VM by opening the TIES.vmx file in VMWare Player. VMWare may ask you if you moved or copied this VM snapshot. You should answer “copied”.

Ubuntu Login Details

Step 4: Launch the TIES Client

To launch TIES client, click on TIES icon in the dock on the left hand side. You can also invoke it from the command line by typing “ties”. TIES Client gives you a choice to login into Production or Test Networks. To start off we will use the Test Network as it is loaded with some test data for you to try TIES out with. Use the Test Researcher credentials below to login to the Test Network.

TIES Login Details

Production Network – is the location where your real data should be loaded. Test Network – is preloaded sample data that you can browse to test the client.

Step 5: Try a search

Since the Test Network is loaded with test data, only certain search terms will be found. You can search for “core biopsy” to start things out. That should get you about 44 hits.

Loading your own documents in TIES

Node Administration

TIES Node

TIES Node is the back-end system that handles all major aspects of the TIES system. To start/stop TIES Node type:

sudo ties-node <start|stop|status>

enter ‘ties’ when prompted for a password

TIES Pipelines

TIES pipelines are stand alone processes that run in the background and process data. To start/stop TIES Pipelines type:

sudo ties-pipelines <start|stop|status>

enter ‘ties’ when prompted for a password You can also start/stop individual pipelines by typing:

ties-HL7-pipe, ties-DeID-pipe, ties-coder-pipe or ties-indexer-pipe

TIES Data

TIES support data in HL7 format. For more details please read this: http://ties.dbmi.pitt.edu/documentation/for-installers/loading-your-data To get started with processing your own data, place HL7 files into

/opt/ties/HL7

A sample HL7 file is located in

/opt/ties/sampledata/HL7

TIES data is stored in MySQL database. You are welcome to use MySQL Workbench to explore the data in the database MySQL DB User:     ties/ties MySQL DB Admin:    root/ties To completely delete all data from production database type:

clear_ties_data

TIES Directory Structure